--- Log opened Wed Oct 18 00:00:49 2017
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05:51 < kanzure> .tw https://twitter.com/briscoejames/status/920226046032662528
05:51 < yoleaux> Wow. Up to 95% knock-in efficiencyq of targeted large insertions in mouse embryos using 2C-HR-CRISPR https://www.biorxiv.org/content/early/2017/10/16/204339 (@briscoejames)
05:51 < kanzure> "Efficient generation of targeted large insertions in mouse embryos using 2C-HR-CRISPR" https://www.biorxiv.org/content/early/2017/10/16/204339
05:52 < kanzure> "Rapid sequential in situ multiplexing with DNA exchange imaging in neuronal cells and tissues" http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.7b02716 https://twitter.com/eboyden3/status/919584573268389889
05:54 < kanzure> .tw https://twitter.com/antonioregalado/status/919332672392056832
05:54 < yoleaux> Is the age of Do-it-on-Yourself CRISPR coming? And what will it mean? (THREAD) #DIY #DIYbio (@antonioregalado)
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05:58 < kanzure> .tw https://twitter.com/antonioregalado/status/919344486953693184
05:58 < yoleaux> 14/ This year Salk scientists dosed decrepit mice w/ just four "embryonic" gene factors. They seemed younger after https://www.salk.edu/news-release/turning-back-time-salk-scientists-reverse-signs-aging/ (@antonioregalado, in reply to tw:919343112882880513)
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06:11 < kanzure> .tw https://twitter.com/AW_NGS/status/920288444143763456
06:11 < yoleaux> #Utrechtnanopore enormous diversity in viruses. More than stars in the galaxy. @nanopore helps speed-up identification https://pbs.twimg.com/media/DMWFc_1X0AA6o3R.jpg (@AW_NGS)
06:12 < kanzure> "Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation" https://www.nature.com/articles/s41467-017-01104-3 https://twitter.com/rob_carlson/status/920304581816467456
06:13 < kanzure> (lutz stuff)
06:13 < kanzure> "In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence ...
06:13 < kanzure> ...coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds ...
06:14 < kanzure> ...break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found."
06:19 < kanzure> "Here, we report that MS sequencing of long-coded polymer chains can be achieved through careful macromolecular design. Poly(phosphodiester)s chains containing several bytes of information were synthesized and sequenced. Two important molecular features are implemented in the analyte design: alkoxyamine groups are placed between the bytes and each byte is labeled by a mass tag. In ...
06:19 < kanzure> ...collision-induced dissociation (CID) conditions, the weak NO-C bonds are selectively cleaved, thus leading to a series of mass tag-shifted intact bytes. Afterwards, each byte can be individually activated and easily deciphered by MS3."
06:20 < kanzure> .wik alkoxyamine9
06:20 < yoleaux> kanzure: Sorry, I couldn't find article.
06:20 < kanzure> .wik alkoxyamine
06:20 < yoleaux> "Nitroxide-mediated radical polymerization is a method of radical polymerization that makes use of an alkoxyamine initiator to generate polymers with well controlled stereochemistry and a very low polydispersity index. It is a type of reversible-deactivation radical polymerization." — https://en.wikipedia.org/wiki/Nitroxide-mediated_radical_polymerization
06:20 < kanzure> .wik carbamate
06:20 < yoleaux> "A carbamate is an organic compound derived from carbamic acid (NH2COOH). A carbamate group, carbamate ester (e.g., ethyl carbamate), and carbamic acids are functional groups that are inter-related structurally and often are interconverted chemically. Carbamate esters are also called urethanes." — https://en.wikipedia.org/wiki/Carbamate
06:22 < kanzure> "This polymer was first analyzed by negative mode electrospray ionization (ESI)-MS, which revealed a dominant charge state distribution (Fig. 2a). Among all detected polyanions, the dodeca-anion [M-12H]12− was selected for MS2: because it contains, on average, three deprotonated phosphate groups per byte, its dissociation leads to byte fragments at a preferential −3 charge state.  .... ...
06:22 < kanzure> ...Collision energy was hence raised to promote consecutive dissociations of large primary product ions, in order to form secondary fragments that each contains one inner-chain byte. Energy has, however, to remain below dissociation threshold of phosphate bonds to prevent inner-byte fragmentation. In such conditions, a very clear bytes pattern can be observed in the resulting MS2 spectrum (Fig. ...
06:22 < kanzure> ...2b). Each byte appears predominantly as a trianion (while remaining as minor signals at −2 or −4 charge states) and the byte tags lead to unambiguous mass shifts that allow identification of their initial location in the chain (Supplementary Table 3)."
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06:39 < kanzure> .tw https://twitter.com/GeneMods/status/920057271345872897
06:39 < yoleaux> 10K Genes Brainstorming Session | GeneMods | 10.18.17: http://youtu.be/J0abA635lDI?a via @YouTube (@GeneMods)
06:40 < kanzure> .title http://youtu.be/J0abA635lDI?a
06:40 < yoleaux> 10K Genes Brainstorming Session | GeneMods | 10.18.17 - YouTube
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08:59 < heath> kanzure: the nature link for "Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation" isn't forwarding the user to a specific paper
08:59 < heath> do you have the doi?
09:00 < kanzure> works for me
09:00 < kanzure> https://www.nature.com/articles/s41467-017-01104-3.pdf
09:12 < kanzure> https://eev.ee/blog/2017/10/07/javascript-got-better-while-i-wasnt-looking/
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09:31 < kanzure> fltrz: welcome back.
09:31 < fltrz> hi
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10:11 < kanzure> fltrz: what's up
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10:16 < fltrz> scatterbraining again, worked a bit with fpga (duct taping serial port and spi controller with a minimal state machine for reading out the flash memory of the kinect)
10:17 < fltrz> also looking up op-amp noise theory (and hence reviewing different interpretations of johnson nyquist noise and shot noise etc)
10:17 < fltrz> the local electronics parts store only sells shit op-amps
10:17 < fltrz> so I will have to order some online
10:20 < fltrz> the op-amp is for making a simple photodiode geiger counter, for giggles, sometimes you just need to reward yourself with fun projects
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12:07 < heath> https://wyss.harvard.edu/art-advancing-science-at-the-nanoscale/
12:07 < heath> move at the bottom
12:07 < heath> s/move/movie
12:26 < kanzure> .title https://www.youtube.com/watch?v=zDotDiK2UuY&feature=youtu.be&t=50
12:26 < yoleaux> D-Wave Lab Tour Part 1 (of 3) - The Infrastructure of the D-Wave Quantum Computer - YouTube
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13:06 < kanzure> .title http://space.mit.edu/home/tegmark/wmap.html
13:06 < yoleaux> The Universes of Max Tegmark
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14:39 < mindsForge> .title https://gizmodo.com/this-guy-just-injected-himself-with-a-diy-hiv-treatment-1819659724?rev=1508360147623
14:39 < yoleaux> This Guy Just Injected Himself With a DIY HIV Treatment on Facebook Live
14:40 < mindsForge> does "Ascendence Biomedical" hang out here ?
14:41  * mindsForge looks around suspiciously
14:41 < kanzure> not to my knowledge
14:46 < rpifan> did it work tho
14:46 < nmz787> apparently no one is sending bionet genes for free synthesis
14:47 < nmz787> I heard keoni is bummed
14:47 < rpifan> whats that mean
14:47 < nmz787> reddit.com/r/bionet
14:47 < nmz787> (if I remember my reddit sub syntax correctly)
14:50 < rpifan> so what do u get from it
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15:04 < kanzure> nmz787: i guess we can make up some shit
15:04 < kanzure> to send to them for dna synthesis
15:04 < kanzure> i dunno, how about a virus
15:05 < kanzure> whole bunch of genes we could pick http://diyhpl.us/wiki/genetic-modifications/
15:05 < rpifan> well
15:05 < kanzure> maybe some bioluminescen-- eh who am i
15:06 < kanzure> maybe a klotho variant
15:14 < kanzure> "Two other variants positioned in the 5' end of the gene, rs398655 and rs562020, were associated with better cognitive function independently of KL-VS"
15:23 < rpifan> fix the hiv and cancer
15:27 < kanzure> that's your job not mine, you do it
15:32 < rpifan> idk how
15:32 < rpifan> u know how to make geens
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17:22 < kanzure> .title https://www.youtube.com/watch?v=UTHiGxjAR4A
17:22 < yoleaux> Circling behavior triggered by optogenetic stimulation - YouTube
17:27 < kanzure> .wik brian wowk
17:27 < yoleaux> "Brian G. Wowk, Ph.D. is a medical physicist and cryobiologist known for the discovery and development of synthetic molecules that mimic the activity of natural antifreeze proteins in cryopreservation applications, sometimes called "ice blockers"." — https://en.wikipedia.org/wiki/Brian_Wowk
17:27 < kanzure> ".. These systems were described by Wowk in the chapter "Phased Array Optics" in the 1996 anthology Nanotechnology: Molecular Speculations on Global Abundance [1]."
17:28 < kanzure> re: http://phased-array.com/
17:28 < kanzure> "molecular speculations on global abundance" https://web.archive.org/web/20060118094514/http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=5039
17:29 < kanzure> http://libgen.io/book/index.php?md5=7251C9B170AE56E15303A79EAF39BCFB
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17:30 < kanzure> hmm ESR is cited in this book
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17:32 < kanzure> http://diyhpl.us/~bryan/papers2/nanotech/BC%20Crandall-Nanotechnology_%20molecular%20speculations%20on%20global%20abundance-MIT%20Press%20(1996).pdf
17:35 < kanzure> wat "New techniques for terrorism and assassination, such as food that, once swallowed, turns into razor blades."
17:36 < kanzure> "Paint-on watches and thermometers"
17:36 < kanzure> "Tool-less construction material that breaks apart along a perfect seam on command—and glues together seamlessly."
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18:08 < mindsForge> https://www.youtube.com/watch?v=vk3nLGNgyxw micro-array of nematodes feeding them genetically modified bacteria
18:11 < mindsForge> 3:33 -- he becomes the worm god
18:26 < kanzure> .title https://news.ycombinator.com/item?id=15503451
18:26 < yoleaux> Why Cryonics Makes Sense (2016) | Hacker News
18:26 < kanzure> https://waitbutwhy.com/2016/03/cryonics.html
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19:12 < juul> am i misunderstanding something or will the new google tpu cloud with its nearly 90 teraflops be enough to simulate ~2 human brains in real time?
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22:50 < nmz787> fltrz: is that using a PIN diode?
22:50 < nmz787> fltrz: I have gone far far down the rabbit hole of op-amp and transimpedance amps before, which spirals into analog in general
22:51 < fltrz> nmz787: yes, BPW34 PIN photodiode, http://opengeiger.de/index_en.html
22:51 < nmz787> I've tried making some stuff with that
22:51 < nmz787> for detecting x-ray
22:51 < nmz787> based on the jameco kit
22:51 < nmz787> laid out a custom PCB, but it didn't work on first testing, and I kinda never debugged it
22:52 < fltrz> yes I have worked with opamps, TIA before too. its just the first time I decided to look up the exact total noise for op-amp amplifier circuits
22:52 < fltrz> will look up jameco kit thx
22:52 < nmz787> ah, I haven't really worked with them before
22:52 < nmz787> so it was kinda jumping the deep end of the pool
22:52 < nmz787> jumping in *
22:52 < fltrz> nmz787: you ordered a kit, or took the circuits and chose your own components?
22:52 < nmz787> both
22:53 < nmz787> I built the kit first
22:53 < fltrz> that worked?
22:53 < nmz787> but I was trying to use it for a more sensitive purpose
22:53 < fltrz> right
22:53 < nmz787> eh, I didn't really test it but with optical signal and an oscilloscope
22:53 < nmz787> it seemed to do something
22:53 < nmz787> when it got bright enough, my scope triggered
22:53 < fltrz> could you show me the circuit, and the components you used (for the increased sensitivity)
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22:55 < fltrz> you can check the amplification and frequency response with very low intensity optical light, but why not just hold some old smokedetector or chalk/banana etc close by?
22:56 < fltrz> yesterdat I grok-ed the total noise in the 3 most common opamp configurations
22:56 < fltrz> so I can calculate the rms noise if you show me your circuit
22:57 < fltrz> nmz787: jameco appears to be the same one as on instructables?
22:58 < nmz787> fltrz: do you have kicad?
22:58 < fltrz> nmz787: kicad is fine
23:11 < nmz787> fltrz: https://github.com/nmz787/xray_detector
23:13 < nmz787> fltrz: I ordered that PCB that I link to, then decoupled the photodiode and jfet (I think) with a cable (the head folder) and used the same PCB with those components depopulated
23:15 < nmz787> was testing it in a focused ion beam, to try and detect x-rays produced when the gallium metal beam hit other metals.... so disconnecting the electronics was for space reasons, and also since it was in a vacuum, for heat reasons (though I just assumed it might possibly get too hot, didn't have any calculations or experience to back it up)
23:16 < nmz787> this was in april 2016 :/
23:16 < nmz787> sorta haven't worked on it since then
23:16 < nmz787> fltrz: any input/feedback/improvements on it would be great
23:17 < nmz787> fltrz: yeah I think the instructables might be the same... I remember something about some kid was the one who wrote it and also made a video
23:20 < fltrz> what cable did you use?
23:20 < fltrz> coax?
23:21 < fltrz> also, I know the noise calculation for op amp circuits, but I should look up the same for the JFET front-end transistor
23:25 < fltrz> what output/information did you desire from the detector? analog signal proportional to count rate, pulses per gamma, or pulses with pulseheights corresponding to gamma energy?
23:27 < nmz787> ideally a change in frequency or something, so you could hook it up to a buzzer/LED/analog-to-digital readout
23:27 < nmz787> spectroscopy was also an interest
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23:28 < nmz787> using the LPC4370 with 80 MSPS ADC embedded in it ($20 dev board is the LPC Link V2)
23:28 < nmz787> cable was just some twisted pair wires in a foil shield
23:29 < fltrz> nmz787: you see the picture at http://opengeiger.de/index_en.html ? thats the current pulse from the photodiode, as you can see, roughly the same pulse shape occurs with different pulse heights
23:29 < nmz787> but inside that foil was also the power and ground signal too
23:29 < fltrz> the pulse heights correspond to the energy of the photon
23:29 < nmz787> err, maybe it was just 3 wires, power ground and signal, I can't remember
23:30 < fltrz> yes with ADC you would get those out
23:32 < fltrz> so the second half of the lm358 is the sound/led signal generation.. lets call this the human interface
23:33 < fltrz> when you probed the signal on an oscilloscope, what signal did you probe? I assume GND<->AMP1_OUT
23:34 < fltrz> at that point the photodiode should be shielded with a thin aluminum foil (opengeiger.de uses adhesive aluminum foil covering a hole drilled in the aluminum box)
23:35 < nmz787> I was trying both
23:35 < nmz787> I remember thinking the second op-amp was a second stage
23:35 < fltrz> but I am still unsure if this jameco circuit sees individual pulses, or average current
23:35 < nmz787> more of a buffer
23:36 < nmz787> the cabled-version was all taped with foil and just barely exposed at the clear epoxy/plastic face
23:36 < nmz787> I assumed that I'd get little photons inside the focused ion beam's vacuum chamber I was testing with
23:37 < nmz787> on my desk though, I was just using some dark cover
23:37 < nmz787> I can't remember
23:37 < nmz787> maybe it was foil
23:39 < fltrz> can there be visible light in the vacuum chamber? hmm
23:40 < nmz787> yeah
23:40 < nmz787> it's possible
23:40 < nmz787> x-rays are just one wavelength I guess, that are produced with i.e.
23:41 < nmz787> .wik bremsstrahlung radiation
23:41 < yoleaux> "Bremsstrahlung (German pronunciation: [ˈbʁɛmsˌʃtʁaːlʊŋ] ( listen), from bremsen "to brake" and Strahlung "radiation"; i.e., "braking radiation" or "deceleration radiation") is electromagnetic radiation produced by the deceleration of a charged particle when deflected by another charged particle, typically an electron by an atomic nucleus." — https://en.wikipedia.org/wiki/Bremsstrahlung_radiation
23:41 < nmz787> or .wik pixe
23:41 < nmz787> .wik particle induced xray emission
23:41 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
23:41 < nmz787> .wik particle induced xray emission
23:41 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
23:41 < nmz787> .wik Particle-induced X-ray emission
23:41 < yoleaux> "Particle-induced X-ray emission or proton-induced X-ray emission (PIXE) is a technique used in the determining of the elemental make-up of a material or sample. When a material is exposed to an ion beam, atomic interactions occur that give off EM radiation of wavelengths in the x-ray part of the electromagnetic spectrum specific to an element." — https://en.wikipedia.org/wiki/Particle-induced_X-ray_emission
23:43 < fltrz> nmz787: you really want to block all visible light, because the photodiode is very responsive to it
23:44 < nmz787> well with the cabled probe, I didn't seem to get any signal the last time i tested it in the fib
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23:45 < fltrz> you can use visible light (i.e. a very dimly lit diode enclosed together in lightproof casing) for veryifying the amplifier stages (like frequency response etc)
23:46 < fltrz> but your use case sounds very constrained, space / heat dissipation wise
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23:47 < fltrz> how thick is the vacuum chamber?
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23:53 < fltrz> to be honest, if you want to keep the option of spectroscopy open, I would stay away from the jfet transistor frontend, its hard to beat the op-amp designers
23:54 < fltrz> the op-amps will have linear response to energy, and the noise will be far lower if you choose an op-amp with tiny (order fA/sqrtHz) current noise
23:55 < nmz787> hmm, ok
23:55 < nmz787> the vacuum chamber is probably an inch of stainless steel
23:56 < nmz787> with a viton or something gasket around the side that opens
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23:56 < nmz787> I didn't really know about all the parameters and how they connected, especially when it came to all the quantum efficiency stuff
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23:57 < nmz787> using the PIN diode out-of-spec means the mfg doesn't provide that sort of characterization info (so they don't even imply a guarantee, probably)
23:58 < fltrz> correct, and you will want to calibrate the PIN anyway
--- Log closed Thu Oct 19 00:00:37 2017